Process CERB
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function process_CERB() %created by Erik Stassinos 6-11-2013 %This is the global script which calls all COPS processing scripts %2-27-2014 modified to check for cast ID matrix %2-27-2014 modified to check if depths are good % % %============= % check if files have already been generated starttime = tic; ml = fopen('mCElist_prr.txt'); if ml ~= -1 disp('most processing has already been started') disp('remove all files other than C*.lcd files to restart') disp('this will be changed to adapt to processing steps already implemented') yorn = input('Do you want to remove files and start over? y or n ','s') yn = lower(yorn) if strncmp(yn,'n',1) == 1 fclose(ml); return end if strncmp(yn,'y',1) == 1 delete a* delete A* delete b* delete r* delete t* delete m* delete K* delete l* delete 'slist.txt' delete 'Clist.txt' pause(3) end end prrfile('C') %changed from P list 6/24/2013 movefile('Clist_prr.txt','list_prr.txt') %changed from P list 6/24/2013 %========================= %%%CERBbt_E %========================= %%%pause %CERBERUS PARAMS: Master_FrameNumber LuZDepth %opens list_prr.txt inside auto_bt. %%auto_bt('Master_FrameNumber','LuZDepth') %========================= %========================= %castid check plist = fopen('list_prr.txt'); while ~feof(plist) r = fgets(plist); t = textscan(r,'%s'); p = char(t{1,:}); castcheck = fopen(p); for i = 1:50 line = fgets(castcheck); if strncmp(line,'castid',6) == 1 found_castid =1; end end end if exist('found_castid') disp('cast id matrix present') fclose(castcheck) else %CERBbt_E auto_bt('Master_FrameNumber','LuZDepth') end fclose(plist); %========================= %========================= num =1; prrfile('C'); %creates list of prr files "P" %changed from P list 6/24/2013 %changed back to lowercase p list 9-18-2013 prlist = fopen('Clist_prr.txt');%changed from P list 6/24/2013 %changed back to lowercase p list %9-18-2013 %=========first math sequence while ~feof(prlist) newl(num,:) = fgets(prlist); num = num +1; end frewind(prlist) for i = 1:num -1 filename = newl(i,:); %domath(filename,'s','LuZDepth',0,0.486,'depth_Lu') %changed 6-24-13 domath (filename,'s','LuZDepth',0,0.4,'depth_ed') end cpsfile('mCE') mlist = fopen('mCElist_prr.txt'); num =1; %==============radQC sequence %compares data to limits specified in Copsrqclist.txt while ~feof(mlist) newl2(num,:) = fgets(mlist); num = num +1; end %disp('Copy rqclist.txtfrom a previous processing example and update to this folder') %disp('Press return to continue') %pause for i = 1:num -1 filename = newl2(i,:); %path = '/home/data65/pb/REPROCESS_2010/PRR/rqclist.txt'; path = '/home/oceancolor/Plumes_and_Blooms/workspace/eriks/CERBERUS/CERBrqclist.txt'; COPSradQC(filename,path); end cpsfile('rqcm') rlist = fopen('rqclist_prr.txt'); num =1; %============doKQ sequence while ~feof(rlist) newl3(num,:) = fgets(rlist); num = num +1; end for i = 1:num -1 infile = newl3(i,:); infile = strtrim(infile); CERBdoKQ(infile,'m','EdZ412',10,0.005,0.02) %-m 2Es412 10 0.005 0.02 end cpsfile('Krqc') Klist = fopen('Krqlist_prr.txt'); num =1; %============angQ sequence while ~feof(Klist) newl4(num,:) = fgets(Klist); num = num +1; end %==>file check for i = 1:num -1 %======Check if there are actually files to process infile = newl4(i,:); if infile ==-1 disp('No files in Klist for angQ!?!?') disp('Ending program') return end %==>end file check infile = strtrim(infile); CPSangQ(infile,'EdZPitch','EdZRoll','EdZ443','LuZ443'); %hard coded range is 10 deg, flag is "2" changed 12-3-12 %keyboard CPSangQ(strcat('an',infile),'EdZPitch','Ed0Roll','EdZ443','LuZ443'); end cpsfile('anKr'); movefile('anKlist_prr.txt','list_prr.txt') % % %pause(5) %=======split cast and binning %prr_split %takes list_prr.txt %==========replaced with split file splist = fopen('list_prr.txt'); num =1; while ~feof(splist) newlA(num,:) = fgets(splist); num = num +1; end for i = 1:num -1 infile = newlA(i,:); infile = strtrim(infile); prr_split_file(infile); end list_file = 'slist.txt'; bincolnum =2; %COPS depth column %%%%prr_binner(list_file,bincolnum) % % %prr_bincheat(list_file,bincolnum); % % %cpsfile('banK'); % % %banlist = fopen('banlist_prr.txt'); %binned list fclose all banlist = fopen('slist.txt'); num =1; while ~feof(banlist) var = strtrim(fgets(banlist)); newl5(num,:) = var;% fgets(banlist) num = num +1; end for i = 1:num -1 infile = newl5(i,:); infile = strtrim(infile); %doKQ(infile,'m','2Es412',10,0.005,0.02) %-m 2Es412 10 0.005 0.02 %========bscalc sequence CERBbscalcloop(infile) %calls bscalc end %%movefile('banlist_prr.txt','list_prr.txt') cpsfile('bsanK') %bsmlist = fopen('list_prr.txt'); %binned list bsmlist = fopen('bsalist_prr.txt'); %binned list num =1; %==========mathloop squence while ~feof(bsmlist) newl6(num,:) = fgets(bsmlist); num = num +1; end for i = 1:num -1 infile = newl6(i,:); infile = strtrim(infile); %mathloop('bsbanKrqcmP101216E.lcd.1') COPSmathloop(infile) end % % infile % % % % % % cpsfile('mbs') movefile('mbslist_prr.txt','list_prr.txt') mblist = fopen('list_prr.txt'); %binned list num =1; while ~feof(mblist) newl7(num,:) = fgets(mblist); num = num +1; end parfor i = 1:num -1 infi = newl7(i,:); infi = strtrim(infi); %kcloop('mbsbanKrqcmP101216E.lcd.1') COPSkcloop(infi) %used to be bbopkc end mkdir final movefile('kcmbs*',[pwd,'/final']) delete temp* % % % % % % % % elapsed = toc(starttime) disp('Done!')